OBJECTIVES: To evaluate the cost-effectiveness of CYP2C9 genotyping for the management of anticoagulation therapy in patients newly started on warfarin from the provider's perspective. METHODS: A decision tree was designed to simulate, over 12 months, the outcomes of patients newly started on warfarin associated with two alternatives: 1) no genotyping (standard care group); and 2) CYP2C9 genotyping prior to initiation of warfarin therapy (genotyping group). Each alternative could lead to three possible outcomes: No event, bleeding, and thromboembolic event (TE). Patients in the standard care group would receive standard care of the anticoagulation clinic (AC). In the genotyping group, intensified anticoagulation service would be provided to patients with at least one variant CYP2C9 allele while others would receive standard AC care. The intensified AC service was assumed to reduce all event rates by 50% and cost more than standard service by 50%. The prevalence of CYP2C9 polymorphism and event rates was derived from literature. Cost of standard AC service and management of events were estimated from the literature and the Diagnosis-Related Groups charges. Sensitivity analysis was conducted to examine the robustness of the model. RESULTS: The cost per patient-year and event-free rate per 100 patient-year of the genotyping group and the standard care group were USD 1729 and 89%, and, USD 2068 and 85%, respectively. One-way sensitivity analysis showed that the model was sensitive to variation of two variables: rate of bleeding in patients with at least one variant CYP2C9 allele (threshold value = 0.04 events per 100 patient-year) and the reduction of bleeding rate in patients with at least one variant CYP2C9 allele with the intensified service (threshold value = 10%). CONCLUSION: The genotyping group was less expensive and more effective than the standard care group for the management of anticoagulation therapy in patients newly started on warfarin.